Application of micro-resonator is limited by different types of surface inhomogeneity. The 1-th derivative of inhomogeneity (i.e. Δrˊ(φ)) affects the wave transport as well as the height of inhomogeneity (i.e. Δrˊ(φ)). A method based on orthogonal decomposition is proposed to analysis both scattering mechanism respectively. Then surface roughness effect on Q-factor of micro-disk waveguide gallery mode (WGM) resonator is investigated with our method and the analysis fits well with FDTD simulation results.